Bolivia says it will call in Venezuela's acting ambassador to complain about what it considers interference in its internal affairs.
Bolivia's Evo Morales is considered a Chavez-style candidate
Venezuelan diplomat Azael Galero compared the Bolivian right-wing candidate for next month's elections, Jorge Quiroga, to Pontius Pilate.
He said Mr Quiroga was defending the "interests of the empire", adding: "you are either with Chavez or with Bush".
Venezuela President Hugo Chavez is also locked in a diplomatic row with Mexico.
The Bolivian foreign ministry said it was calling in Mr Galero to express the government's worries about his comments.
"It is an intromission in a democratic and transparent electoral process," a statement said.
Earlier, Mr Quiroga had accused Mr Chavez of trying to trick Bolivians with false promises.
Mr Chavez is backing the left-wing front-runner Evo Morales, a former coca-growers' leader known for his strong anti-US stance.
Correspondents describe Mr Morales, an Aymaran Indian, as a Chavez-style candidate.
Meanwhile, the diplomatic dispute between Venezuela and Mexico has seen no signs of abating.
Venezuelan Vice-President Jose Vicente Rangel said that Mexico should not bother waiting for an apology for Mr Chavez's strong criticism of his Mexican counterpart, Vicente Fox.
Both countries withdrew their ambassadors from each other's capitals after a row over free trade led to bitter exchanges.
The row began early November, after Mexico supported a failed US bid to relaunch the Free Trade Area of the Americas (FTAA) at the Summit of the Americas in Argentina.